US10927386B2 - Compositions and methods for Peronospora resistance in spinach - Google Patents

Compositions and methods for Peronospora resistance in spinach Download PDF

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US10927386B2
US10927386B2 US14/632,871 US201514632871A US10927386B2 US 10927386 B2 US10927386 B2 US 10927386B2 US 201514632871 A US201514632871 A US 201514632871A US 10927386 B2 US10927386 B2 US 10927386B2
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plant
resistance
spinach
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Bart Willem Brugmans
John Meeuwsen
Claudia Nooyen
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Seminis Vegetable Seeds Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8279—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
    • A01H1/04—Processes of selection involving genotypic or phenotypic markers; Methods of using phenotypic markers for selection
    • A01H1/045—Processes of selection involving genotypic or phenotypic markers; Methods of using phenotypic markers for selection using molecular markers
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H5/00—Angiosperms, i.e. flowering plants, characterised by their plant parts; Angiosperms characterised otherwise than by their botanic taxonomy
    • A01H5/12—Leaves
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H6/00—Angiosperms, i.e. flowering plants, characterised by their botanic taxonomy
    • A01H6/02—Amaranthaceae or Chenopodiaceae, e.g. beet or spinach
    • A01H6/028—Spinacia oleracea [spinach]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/13—Plant traits
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the invention relates to the field of plant breeding and, more specifically, to methods and compositions for producing spinach plants with resistance to downy mildew.
  • Downy mildew caused by the plant pathogen Peronospora farinosa f . sp. Spinaciae (Pfs), is an economically important disease of spinach worldwide, particularly for Spinacia oleracea , the most commonly cultivated spinach species.
  • DM downy mildew
  • the invention provides a Spinacia oleracea spinach plant comprising in its genome allele A, as described herein.
  • the invention provides a Spinacia oleracea spinach plant comprising in its genome a heterozygous combination of alleles that confers broad-spectrum resistance to Peronospora farinosa f . sp. Spinaciae .
  • the broad-spectrum resistance comprises resistance to at least 10 races of Peronospora farinosa f . sp. spinaciae (Pfs).
  • the allele that confers broad-spectrum resistance is a combination of alleles which is selected from the group consisting of allele A, allele Vt, and allele C.
  • the combination of alleles comprises alleles A and C and the plant is resistant to at least Peronospora farinosa f . sp. Spinaciae races 7, 8, 10, 11, 12, 14, and isolate UA4712; the combination of alleles comprises alleles A and Vt, and the plant is resistant to at least Peronospora farinosa f . sp. Spinaciae races 7, 8, 10, 11, 12, 13, and 14; or the combination of alleles comprises alleles C and Vt, and the plant is resistant to at least Peronospora farinosa f . sp. Spinaciae races 7, 8, 10, 11, 12, 13, and isolate UA4712.
  • representative samples of seed comprising allele A, allele C, and allele Vt have been deposited under ATCC Accession No. PTA-120472, ATCC Accession No. PTA-12486, and ATCC Accession No. PTA-12041, respectively.
  • the allele A, allele C, and/or allele Vt is genetically linked to at least one sequence selected from the group SEQ ID NOs:1-25.
  • a plant of the invention comprises an allele A, allele C, and/or allele Vt that shares a genetic source for said allele with seed deposited under ATCC Accession Nos. PTA-120472, ATCC Accession No. PTA-12486, or ATCC Accession No. PTA-12041.
  • a plant of the invention may be an inbred or a hybrid.
  • the invention provides a seed that produces such a plant, or a plant part of such a plant.
  • the plant part is selected from the group consisting of an embryo, meristem, cotyledon, pollen, leaf, anther, root, pistil, flower, cell, and stalk.
  • the invention provides a food product comprising the harvested leaves of such a spinach plant.
  • the invention provides a Spinacia oleracea spinach plant comprising in its genome a heterozygous combination of alleles that confers broad-spectrum resistance to Peronospora farinosa f . sp. Spinaciae , wherein one allele confers recessive resistance to Peronospora farinosa f . sp. Spinaciae races 7 and 13.
  • the broad-spectrum resistance comprises resistance to at least 10 races of Peronospora farinosa f . sp. spinaciae (Pfs).
  • one allele is allele Vt and the other allele is allele C
  • one allele is allele A and the other is allele Vt
  • one allele is allele A and the other is allele C.
  • the invention provides a method of producing a spinach plant with broad spectrum resistance to Peronospora farinosa f . sp.
  • Spinaciae comprising: (a) crossing a first spinach plant comprising in its genome a first allele selected from the group consisting of A, Vt, and C, with a second spinach plant comprising in its genome a second allele selected from the group consisting of A, Vt, and C, to produce a population of hybrid progeny plants; and (b) selecting at least one hybrid progeny plant from said population that comprises a combination of said first allele and said second allele that confers broad-spectrum resistance to Peronospora farinosa f . sp. Spinaciae .
  • the method further comprises production of a population of hybrid plants.
  • the first spinach plant comprises allele A and the second spinach plant comprises allele C; or the first spinach plant comprises allele A and the second spinach plant comprises allele Vt; or the first spinach plant comprises allele C and the second spinach plant comprises allele Vt.
  • the invention provides a hybrid progeny plant produced by such a method.
  • the first allele of the plant is allele A and the second allele is allele C; or the first allele is allele A and the second allele is allele Vt; or the first allele is allele C and the second allele is allele Vt.
  • the invention provides a method of introducing resistance to Peronospora farinosa f . sp. Spinaciae in a spinach plant comprising: (a) crossing a first spinach plant comprising in its genome a first allele selected from the group consisting of A, Vt, and C, with a second spinach plant comprising in its genome a second, distinct allele; (b) selecting at least one progeny plant that comprises said first allele for resistance to Peronospora farinosa f . sp. Spinaciae based on the presence in the genome of the plant of a sequence selected from SEQ ID NOs:1-25.
  • the method comprises detecting in the genome of said plant at least two polymorphic nucleic acid sequences selected from the group consisting of SEQ ID NOs:1-25, wherein the presence of the polymorphic nucleic acid sequences are indicative of the presence in the plant of at least two alleles conferring resistance to Peronospora farinosa f . sp. Spinaciae selected from of alleles A, Vt, and C.
  • the invention provides a spinach plant, cell or cell containing plant part comprising at least two polymorphic DNA sequences which are associated with different alleles from among alleles A, Vt, and C.
  • a spinach plant, cell or cell containing plant part are provided comprising at least two DNA sequences that are represented in different groups from among those designated (a), (b) and (c), said groups being made up as follows: (a) a DNA sequence comprising SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:16, SEQ ID NO:19, or SEQ ID NO:22; (b) a DNA sequence comprising SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:9, SEQ ID NO:12, SEQ ID NO:15, SEQ ID NO:18, SEQ ID NO:21, or SEQ ID NO:22; and (c) a DNA sequence comprising SEQ ID NO:3, SEQ ID NO:
  • SEQ ID NO:1 DNA sequence corresponding to scaffold SF63815 and diagnostic for allele C.
  • SEQ ID NO:2 DNA sequence corresponding to scaffold SF63815 and diagnostic for allele A.
  • SEQ ID NO:3 DNA sequence corresponding to scaffold SF63815 and diagnostic for allele Vt.
  • SEQ ID NO:4 DNA sequence corresponding to scaffold SF59002 and diagnostic for allele C.
  • SEQ ID NO:5 DNA sequence corresponding to scaffold SF59002 and diagnostic for allele A.
  • SEQ ID NO:6 DNA sequence corresponding to scaffold SF59002 and diagnostic for allele Vt.
  • SEQ ID NO:7 DNA sequence corresponding to scaffold SF59002 and diagnostic for allele A.
  • SEQ ID NO:8 DNA sequence corresponding to scaffold SF59002 and diagnostic for allele Vt.
  • SEQ ID NO:9 DNA sequence corresponding to scaffold SF95487 and diagnostic for allele C.
  • SEQ ID NO:10 DNA sequence corresponding to scaffold SF95487 and diagnostic for allele A.
  • SEQ ID NO:11 DNA sequence corresponding to scaffold SF95487 and diagnostic for allele Vt.
  • SEQ ID NO:12 DNA sequence corresponding to scaffold SF90906 and diagnostic for allele C.
  • SEQ ID NO:13 DNA sequence corresponding to scaffold SF90906 and diagnostic for allele A.
  • SEQ ID NO:14 DNA sequence corresponding to scaffold SF90906 and diagnostic for allele Vt.
  • SEQ ID NO:15 DNA sequence corresponding to scaffold SF90906 and diagnostic for allele C.
  • SEQ ID NO:16 DNA sequence corresponding to scaffold SF90906 and diagnostic for allele A.
  • SEQ ID NO:17 DNA sequence corresponding to scaffold SF90906 and diagnostic for allele Vt.
  • SEQ ID NO:18 DNA sequence corresponding to scaffold SF34732 and diagnostic for allele C.
  • SEQ ID NO:19 DNA sequence corresponding to scaffold SF34732 and diagnostic for allele A.
  • SEQ ID NO:20 DNA sequence corresponding to scaffold SF34732 and diagnostic for allele Vt.
  • SEQ ID NO:21 DNA sequence corresponding to scaffold SF34732 and diagnostic for allele C.
  • SEQ ID NO:22 DNA sequence corresponding to scaffold SF34732 and diagnostic for allele A.
  • SEQ ID NO:23 DNA sequence corresponding to scaffold SF34732 and diagnostic for allele Vt.
  • SEQ ID NO:24 DNA sequence corresponding to alleles A, C, and Vt of scaffold SF62749.
  • SEQ ID NO:25 DNA sequence corresponding to alleles A, C, and Vt of scaffold SF178637.
  • FIG. 1 Shows alleles A, Vt, and C, which represent three linkage groups assembled from genotypes and phenotypes collected for three mapping populations, as described in Example 3.
  • FIG. 2A and FIG. 2B Show possible breeding methods for development of hybrids and three-way hybrids.
  • FIG. 3 Shows sequence alignments of scaffolds containing polymorphisms corresponding to alleles C, A, and Vt. Polymorphisms between alleles are underlined, and can be used to identify and/or diagnose the presence of downy mildew resistance alleles C, A, and/or Vt in spinach.
  • the present invention provides methods and compositions for development of spinach varieties with resistance to downy mildew (DM).
  • DM downy mildew
  • the invention provides the identification of three distinct alleles from Spinacia oleracea , which have been named A, Vt, and C. These alleles can be used in various combinations to obtain spinach plants with a unique broad-spectrum resistance to DM.
  • the three alleles designated A from spinach line SMBS011-1162M, C from SMB-66-1143M, and Vt from SSB-66-1131M, were identified in Spinacia oleracea and found to provide resistance to existing and emerging DM strains. Each allele was found to have resistance to a specific set of races and/or isolates. The alleles can be used in various combinations to make hybrids with desired DM resistance.
  • allele C was found to confer resistance to races 1, 2, 3, 4, 5, 6, 7, 8, 10 and newly occurring Pfs isolate UA4712, which is the candidate strain for race 15.
  • Allele A was found to confer resistance to Peronospora farinosa (Pfs) races 1, 3, 5, 7, 8, 11, 12, 13 and 14.
  • the resistance to races 7 and 13, unlike most DM races, is inherited in a recessive manner.
  • Allele Vt was found to confer resistance to races 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12 and 13.
  • alleles C and Vt can be present in a spinach plant (i.e., a heterozygous spinach plant) and provide resistance to Pfs races 1-8, 10-13, and to newly occurring Pfs isolate UA4712.
  • alleles A and Vt can be present in a spinach plant and provide resistance to Pfs races 1-8 and 10-14. Allele Vt complements the recessive resistances from allele A.
  • alleles A and C are present together in a spinach plant, the plant is resistant to Pfs races 1-8, 10-12, 14 and UA4712.
  • the alleles can be utilized in any combination to provide desired resistance for a particular market or region.
  • a hybrid with alleles C and Vt exhibits resistance to all Pfs races except Pfs 14. Since Pfs race 14 does not occur in Europe, this hybrid would be fully resistant in that geography.
  • a hybrid with alleles A and Vt exhibits resistance to all Pfs races except isolate UA4712. New isolate UA4712 is found in limited locations, so this hybrid would be fully resistant in many areas.
  • a three-way hybrid is contemplated that is resistant to all described DM races and isolate UA4712.
  • a spinach plant comprising one or two alleles described herein, including, but not limited to, A, C, and Vt, can be crossed with a second, distinct spinach plant comprising a second or third allele including, but not limited to, A, C, and Vt to produce a hybrid spinach plant comprising a beneficial set of alleles as described herein.
  • alleles can be introgressed into selected spinach varieties in any combination to provide a desired resistance to DM.
  • such alleles conferring resistance to DM may be introgressed into any desired genomic background of a specific spinach variety or cultivar.
  • a starting spinach plant containing a given DM resistance allele in accordance with the invention can be self-fertilized a sufficient number of generations to produce an inbred spinach variety that is homozygous for the allele conferring resistance to DM.
  • Such an inbred plant may then be crossed with another spinach plant that comprises a distinct DM resistance allele to consistently produce spinach inbreds and/or hybrids that comprise a combination of alleles conferring a desirable resistance to DM as described herein.
  • a spinach plant exhibiting resistance to DM according to the invention may further be crossed to other spinach plants and selections carried out according to the invention to obtain new DM-resistant spinach inbreds and hybrids with any desired combination of alleles described herein.
  • Non-host resistance to DM may also be found in wild relatives of spinach, such as Spinacia turkestanica and Spinacia tetrandra .
  • genes from wild relatives often result in negative drag for commercial characteristics including yield and quality.
  • the unfavorable alleles found in the wild relatives are often introduced into the elite germplasm together with DM resistance alleles.
  • the present invention describes novel S. oleracea resistance sources, alleles, and markers that provide race-specific and broad-spectrum DM resistance.
  • alleles A, C, and Vt, conferring resistance to DM may be defined as being on spinach linkage group 6 by common markers in sequence scaffolds SF34732 and SF63815 on the distal position and SF59002, SF95487, and SF90906 on the proximal position.
  • Nucleotide sequences associated with and diagnostic for the resistance alleles are provided in SEQ ID NOs:1-25. Polymorphisms between alleles A, C, and Vt are shown in FIG. 3 .
  • alleles providing broad-spectrum resistance to DM may be defined as from, or sharing, a genetic source selected from accessions SMBS011-1162M, SMB-66-1143M, and SSB-66-1131M, representative deposits of seed of which were made with the ATCC under accession numbers PTA-120472, PTA-12486, and PTA-12041, respectively.
  • the invention further provides methods of producing spinach plants with broad-spectrum resistance to DM, as well as spinach plants and parts thereof made by such methods.
  • nucleic acid sequences or genomic markers may be used to identify alleles according to the present invention. These nucleic acid sequences may be used in the identification of polymorphisms or markers genetically linked in a spinach genome to the DM-resistance conferring alleles in accordance with the invention.
  • the invention also provides food products derived from such plants and their method of production.
  • Genetic markers in linkage disequilibrium with DM-resistance alleles of the present invention may permit efficient introduction of DM-resistance into essentially any spinach genome. This also results in significant economization by permitting substitution of costly, time-intensive, and potentially unreliable phenotypic assays. Further, breeding programs can be designed to explicitly drive the frequency of specific favorable phenotypes by targeting particular genotypes. Fidelity of these associations may be monitored continuously to ensure maintained predictive ability and, therefore, informed breeding decisions.
  • one of skill in the art may identify a candidate germplasm source possessing a desirable DM-resistant phenotype, such as from an accession described herein.
  • One embodiment of the invention comprises using the materials and methods of the invention to obtain an allele conferring broad-spectrum resistance to DM from any additional spinach accessions.
  • DM resistance can be introgressed into any other spinach varieties.
  • the techniques of the present invention may be used to identify desirable disease-resistant phenotypes by identifying genetic markers genetically linked to an allele or locus conferring such a phenotype.
  • one of skill in the art may develop molecular marker assays based on, for example, SNPs and/or Indels in the spinach genome.
  • molecular marker assays useful to identify DM-resistant spinach plants according to the invention may be designed based on a sequence scaffold from spinach chromosome 6.
  • Such techniques may also involve phenotypic assays to identify desired plants either alone or in combination with genetic assays, thereby also identifying a marker genotype associated with the trait that may be used for production of new varieties with the methods described herein.
  • the invention provides for the production of cultivated spinach plants comprising a combination of alleles conferring resistance to DM.
  • Successful spinach production depends on attention to various horticultural practices. These include soil management with special attention to proper fertilization, crop establishment with appropriate spacing, weed control, and the introduction of bees or other insects for pollination, irrigation, and pest management.
  • Transplanting can result in an earlier crop compared to a crop produced from direct seeding. Transplanting helps achieve complete plant stands rapidly, especially where higher seed costs, as with triploid seeds, make direct-seeding risky.
  • the present disclosure identifies alleles from cultivated spinach and combinations thereof conferring broad-spectrum resistance to DM, as well as sequence scaffolds from spinach chromosome 6 that can be used for the tracking and introgression of the loci into desirable germplasm, such as by marker-assisted selection and/or marker-assisted backcrossing.
  • the invention provides for the tracking and introduction of any such alleles and/or any combination of such alleles with other resistance loci into a given genetic background.
  • resistance to DM conferred by alleles described herein may be introgressed from one genotype to another via marker-assisted selection. Accordingly, a germplasm source can be selected that has resistance to DM.
  • a breeder may select a spinach plant with resistance to DM, or track such a phenotype during breeding using marker-assisted selection for the region described herein.
  • screens with flanking markers may be sufficient to select progeny carrying desired DM resistance in pedigrees that segregate for a single resistance allele.
  • markers can be complemented by phenotypic screens, for example with differential races showing a compatible interaction with one allele and an incompatible interaction with another, to select for individuals with desired resistance in populations segregating for two or more haplotypes.
  • spinach plants in accordance with the present invention may comprise any heterozygous combinations of allele C, allele A, and allele Vt to confer broad DM resistance.
  • alleles C and Vt can be present in a heterozygous spinach plant and confer resistance to Pfs races 1-8, 10-13, and to newly occurring Pfs isolate UA4712.
  • alleles A and Vt can be present in a spinach plant and confer resistance to Pfs races 1-8 and 10-14, or alleles A and C can be present together in a spinach plant and confer resistance to Pfs races 1-8, 10-12, 14 and UA4712.
  • a three-way hybrid that is resistant to all described DM races and isolate UA4712.
  • a spinach plant comprising one or two alleles as described herein may be crossed with a second, distinct spinach plant comprising a second or third allele as described herein to produce a hybrid spinach plant comprising a beneficial set of alleles as described herein.
  • the process of introgressing a novel resistance gene into acceptable commercial types can be a difficult process and may be complicated by factors such as linkage drag, epistasis, and low heritability.
  • the heritability of a trait is the proportion of the phenotypic variation attributed to the genetic variance, which varies between 0 and 1.0. Thus, a trait with heritability near 1.0 is not greatly affected by the environment.
  • Those skilled in the art recognize the importance of creating commercial lines with horticultural traits having high heritability because these cultivars will allow growers to produce a crop with uniform market specifications.
  • the resistance alleles provided herein can be combined for improved resistance, particularly in fields where mixed populations of DM races may occur.
  • the alleles described herein may be introgressed into parents of a hybrid via marker-assisted and/or phenotypic selection. Breeders may select alleles that mutually complement race-specificity to achieve broad resistance to DM. The described resistance donors are crossed to inbreds with demonstrated combining ability. The F1 resulting from each initial cross is then backcrossed with the recipient genotype, i.e. with the recurrent parent. According to the invention, individuals carrying the resistance in the heterozygous phase are selected using marker-assisted and/or phenotypic selection.
  • This backcross and selection step is repeated, for example, three times. Individuals carrying the desired resistance allele are then self-pollinated, for example, for two generations through single seed descent. A breeder may recover inbred spinach plants carrying the desired resistance allele from the progeny of each pedigree, introduced into the same genetic background as respective recurrent parents, preferably at least 95%, 96%, 97%, 98%, or 99% identical. Commercial, resistant cultivars are generated by crossing parental lines, each with a complementary resistance allele, thereby creating hybrids with superior resistance.
  • multiple resistance donors may be individually crossed to the same recipient genotype.
  • an inbred spinach plant carrying a distinct resistance allele may be obtained that has been introduced into the same genetic background as the recurrent parent, preferably at least 95%, 96%, 97%, 98%, or 99% identical.
  • different resistance alleles may be maintained in the same, fixed genetic background, i.e. in near-isogenic lines.
  • the steps to create inbreds that are near-isogenic for resistance alleles can be applied to both inbred parents of any hybrid.
  • breeders may create three-way hybrids by crossing two near-isogenic lines derived from one parental line to generate an F1 seed parent.
  • the F1 seed parent is crossed with the third parent carrying the complementary resistance allele.
  • the resulting three-way hybrid is uniform, except for a complementary combination of DM resistance alleles.
  • Hybrid plants consistently share the same genetic background as the recurrent parent, preferably at least 95%, 96%, 97%, 98%, or 99% identical, and carry various combinations of resistance alleles.
  • the alleles provided herein allow for the consistent production of commercial varieties with broad DM resistance.
  • the present invention provides alleles that can be used in different combinations to provide spinach plants for each area and/or region with distinct DM populations.
  • a single variety can be obtained with a mix of resistance alleles to reduce pathogen pressure when resistance-breaking races or newly emerging isolates exist.
  • Applicants have discovered three alleles from cultivated spinach, S. oleracea , that when present together in particular combinations in a hybrid (heterozygous) spinach plant, confer broad-spectrum resistance to DM.
  • these alleles were found to be located on spinach chromosome 6 in a locus that may be defined by sequence scaffolds SF34732 and SF63815 on the distal position and SF59002, SF95487, and SF90906 on the proximal position, or sequences at least 95% identical thereto, including sequences at least 96%, 97%, 98%, 99%, or 100% identical thereto, as one of skill in the art would understand that polymorphisms may exist in such regions in different populations.
  • Polymorphisms that may be used to identify or diagnose the presence of resistance alleles C, A, and/or Vt are shown in FIG. 3 .
  • Examples of such nucleotide sequences are provided in SEQ ID NOs:1-25. These sequences may be used in accordance with the invention to identify or diagnose the presence or identity of a particular allele in a plant and thus identify plants that carry resistance to DM.
  • One of skill in the art will further appreciate that many genetic markers can be located throughout the S. oleracea genome, and markers may be developed from SNPs and/or Indels in flanking sequences of the sequences described herein and in other fragments located throughout the S. oleracea genome.
  • markers are useful in identifying the presence or absence of a resistance allele in accordance with the invention.
  • markers in the spinach genome are described in, for example, Khattak et al. ( Euphytica 148:311-318, 2006).
  • Khattak et al. Euphytica 148:311-318, 2006.
  • the identification of alleles and DM-resistance conferring alleles as set forth herein, allows the use of any other such markers in the same region and genetically linked (in linkage disequilibrium) therewith.
  • genomic region, alleles, and polymorphic markers identified herein can be mapped relative to any publicly available physical or genetic map to place the region described herein on such map.
  • additional polymorphic nucleic acids as described herein that are genetically linked to an allele associated with resistance to DM in spinach and that map within about 40 cM, 20 cM, 10 cM, 5 cM, or 1 cM of an allele or a markers associated with resistance to DM in spinach may also be used.
  • markers and allelic states are therefore exemplary.
  • One of skill in the art would recognize how to identify spinach plants with other polymorphic nucleic acid markers and allelic states thereof related to resistance to DM in spinach consistent with the present disclosure.
  • One of skill the art would also know how to identify the allelic state of other polymorphic nucleic acid markers located in the genomic region(s) or linked to an allele or other markers identified herein, to determine their association with resistance to DM in spinach.
  • markers for use in identifying the presence or absence of a resistance allele are markers for use in identifying the presence or absence of a resistance allele.
  • markers in the spinach genome that are not associated with or lack significant genetic linkage to the resistance locus allow the selection of genetic background.
  • One example of background selection is recovery of the genome of a recipient parent in a recurring backcross scheme, an example of which is provided herein.
  • recurrent selection multiple rounds of mating between sibs carrying favorable characteristics are carried out and selections made of progeny, allowing introduction of DM resistance-conferring alleles along with genetic diversity into a pedigree while maintaining favorable attributes of one or more elite parent.
  • markers for spinach distributed genome-wide and that may be used in production of plants according to the methods of the invention are described in, for example, Khattak et al. ( Euphytica 148:311-318, 2006).
  • Khattak et al. Euphytica 148:311-318, 2006.
  • the identification of DM resistance-conferring alleles set forth herein, concurrent with background selection, allows the use of any marker in the same genetic interval and any marker in other genetic intervals of genomic fragments.
  • marker-assisted introgression involves the transfer of a chromosomal region, defined by one or more markers, from one germplasm to a second germplasm.
  • Offspring of a cross that contain an introgressed genomic region can be identified by the combination of markers characteristic of the desired introgressed genomic region from a first germplasm (e.g., germplasm with resistance to DM) and both linked and unlinked markers characteristic of the desired genetic background of a second germplasm.
  • telomere proximal or centromere proximal markers that are immediately adjacent to a larger genomic region comprising the allele or locus can be used to introgress that smaller genomic region.
  • Genetic markers that can be used in the practice of the present invention include, but are not limited to, Restriction Fragment Length Polymorphisms (RFLP), Amplified Fragment Length Polymorphisms (AFLP), Simple Sequence Repeats (SSR), simple sequence length polymorphisms (SSLPs), Single Nucleotide Polymorphisms (SNP), Insertion/Deletion Polymorphisms (Indels), Variable Number Tandem Repeats (VNTR), Random Amplified Polymorphic DNA (RAPD), isozymes, and others known to those skilled in the art. Marker discovery and development in crops provides the initial framework for applications to marker-assisted breeding activities (U.S. Patent Pub.
  • the resulting “genetic map” is the representation of the relative position of characterized loci (polymorphic nucleic acid markers or any other locus for which alleles can be identified) to each other.
  • Polymorphisms comprising as little as a single nucleotide change can be assayed in a number of ways. For example, detection can be made by electrophoretic techniques including a single-strand conformational polymorphism (Orita et al. Genomics, 8(2):271-278, 1989), denaturing gradient gel electrophoresis (Myers EPO 0273085, 1985), or cleavage fragment length polymorphisms (Life Technologies, Inc., Gathersberg, Md. 20877), although the widespread availability of DNA sequencing machines often makes it easier to just sequence amplified products directly.
  • electrophoretic techniques including a single-strand conformational polymorphism (Orita et al. Genomics, 8(2):271-278, 1989), denaturing gradient gel electrophoresis (Myers EPO 0273085, 1985), or cleavage fragment length polymorphisms (Life Technologies, Inc., Gathersberg, Md. 20877), although the widespread availability of DNA sequencing machines often makes it easier to just sequence ampl
  • polymorphic markers serve as a useful tool for fingerprinting plants to inform the degree of identity of lines or varieties (U.S. Pat. No. 6,207,367). These markers form the basis for determining associations with phenotypes and can be used to drive genetic gain.
  • polymorphic nucleic acids can be used to detect in a spinach plant a genotype associated with resistance to DM, identify a spinach plant with a genotype associated with resistance to DM, and to select a spinach plant with a genotype associated with resistance to DM.
  • polymorphic nucleic acids can be used to produce a spinach plant that comprises in its genome a combination of alleles associated with resistance to DM.
  • polymorphic nucleic acids can be used to breed progeny spinach plants comprising a combination of alleles associated with resistance to DM.
  • Certain genetic markers may include “dominant” or “codominant” markers. “Codominant” markers reveal the presence of two or more alleles (two per diploid individual). “Dominant” markers reveal the presence of only a single allele. Markers are preferably inherited in a codominant fashion so that the presence of both alleles at a diploid locus, or multiple alleles in triploid or tetraploid loci, are readily detectable, and they are free of environmental variation, i.e., their heritability is 1.
  • a marker genotype typically comprises two marker alleles at each locus in a diploid organism.
  • the marker allelic composition of each locus can be either homozygous or heterozygous. Homozygosity is a condition where both alleles at a locus are characterized by the same nucleotide sequence. Heterozygosity refers to different conditions of the allele at a locus.
  • Nucleic acid-based analyses for determining the presence or absence of the genetic polymorphism can be used in breeding programs for identification, selection, introgression, and the like.
  • a wide variety of genetic markers for the analysis of genetic polymorphisms are available and known to those of skill in the art. The analysis may be used to select for genes, portions of genes, QTL, alleles, or genomic regions that comprise or are linked to a genetic marker that is linked to or associated with a DM resistance phenotype.
  • nucleic acid analysis methods include, but are not limited to, PCR-based detection methods (e.g., TaqMan assays), microarray methods, mass spectrometry-based methods and/or nucleic acid sequencing methods, including whole-genome sequencing.
  • the detection of polymorphic sites in a sample of DNA, RNA, or cDNA may be facilitated through the use of nucleic acid amplification methods.
  • Such methods specifically increase the concentration of polynucleotides that span the polymorphic site, or include that site and sequences located either distal or proximal to it.
  • Such amplified molecules can be readily detected by gel electrophoresis, fluorescence detection methods, or other means.
  • PCR polymerase chain reaction
  • Polymorphisms in DNA sequences can be detected or typed by a variety of effective methods well known in the art including, but not limited to, those disclosed in U.S. Pat. Nos. 5,468,613; 5,217,863; 5,210,015; 5,876,930; 6,030,787; 6,004,744; 6,013,431; 5,595,890; 5,762,876; 5,945,283; 5,468,613; 6,090,558; 5,800,944; 5,616,464; 7,312,039; 7,238,476; 7,297,485; 7,282,355; 7,270,981; and 7,250,252 all of which are incorporated herein by reference in their entireties.
  • compositions and methods of the present invention can be used in conjunction with any polymorphism typing method to type polymorphisms in genomic DNA samples.
  • genomic DNA samples used include, but are not limited to, genomic DNA isolated directly from a plant, cloned genomic DNA, or amplified genomic DNA.
  • polymorphisms in DNA sequences can be detected by hybridization to allele-specific oligonucleotide (ASO) probes as disclosed in U.S. Pat. Nos. 5,468,613 and 5,217,863.
  • ASO allele-specific oligonucleotide
  • U.S. Pat. No. 5,468,613 discloses allele specific oligonucleotide hybridizations where single or multiple nucleotide variations in nucleic acid sequence can be detected in nucleic acids by a process in which the sequence containing the nucleotide variation is amplified, spotted on a membrane and treated with a labeled sequence-specific oligonucleotide probe.
  • Target nucleic acid sequence can also be detected by probe ligation methods as disclosed in U.S. Pat. No. 5,800,944, where a sequence of interest is amplified and hybridized to probes, followed by ligation to detect a labeled part of the probe.
  • Microarrays can also be used for polymorphism detection, wherein oligonucleotide probe sets are assembled in an overlapping fashion to represent a single sequence such that a difference in the target sequence at one point would result in partial probe hybridization (Borevitz et al., Genome Res. 13:513-523, 2003; Cui et al., Bioinformatics 21:3852-3858, 2005).
  • target sequences On any one microarray, it is expected there will be a plurality of target sequences, which may represent genes and/or noncoding regions wherein each target sequence is represented by a series of overlapping oligonucleotides, rather than by a single probe.
  • This platform provides for high throughput screening of a plurality of polymorphisms. Typing of target sequences by microarray-based methods is disclosed in U.S. Pat. Nos. 6,799,122; 6,913,879; and 6,996,476.
  • Target nucleic acid sequence can also be detected by probe linking methods as disclosed in U.S. Pat. No. 5,616,464, employing at least one pair of probes having sequences homologous to adjacent portions of the target nucleic acid sequence and having side chains which non-covalently bind to form a stem upon base pairing of the probes to the target nucleic acid sequence. At least one of the side chains has a photoactivatable group that can form a covalent cross-link with the other side chain member of the stem.
  • SBE methods include single base extension (SBE) methods.
  • SBE methods include, but are not limited to, those disclosed in U.S. Pat. Nos. 6,004,744; 6,013,431; 5,595,890; 5,762,876; and 5,945,283.
  • SBE methods are based on extension of a nucleotide primer that is adjacent to a polymorphism to incorporate a detectable nucleotide residue upon extension of the primer. In certain embodiments, the SBE method uses three synthetic oligonucleotides.
  • Two of the oligonucleotides serve as PCR primers and are complementary to the sequence of the locus of genomic DNA which flanks a region containing the polymorphism to be assayed.
  • the PCR product is mixed with the third oligonucleotide (called an extension primer), which is designed to hybridize to the amplified DNA adjacent to the polymorphism in the presence of DNA polymerase and two differentially labeled dideoxynucleoside triphosphates. If the polymorphism is present on the template, one of the labeled dideoxynucleoside triphosphates can be added to the primer in a single base chain extension.
  • the allele present is then inferred by determining which of the two differential labels was added to the extension primer. Homozygous samples will result in only one of the two labeled bases being incorporated, and only one of the two labels will be detected. Heterozygous samples have both alleles present and will direct incorporation of both labels (into different molecules of the extension primer), and thus both labels will be detected.
  • SNPs and Indels can be detected by methods disclosed in U.S. Pat. Nos. 5,210,015; 5,876,930; and 6,030,787, in which an oligonucleotide probe having a 5′ fluorescent reporter dye and a 3′ quencher dye covalently linked to the 5′ and 3′ ends of the probe.
  • an oligonucleotide probe having a 5′ fluorescent reporter dye and a 3′ quencher dye covalently linked to the 5′ and 3′ ends of the probe.
  • the proximity of the reporter dye to the quencher dye results in the suppression of the reporter dye fluorescence, e.g. by Forster-type energy transfer.
  • forward and reverse primers hybridize to a specific sequence of the target DNA flanking a polymorphism, while the hybridization probe hybridizes to polymorphism-containing sequence within the amplified PCR product.
  • a DNA polymerase with 5′ ⁇ 3′ exonuclease activity cleaves the probe and separates the reporter dye from the quencher dye resulting in increased fluorescence of the reporter.
  • an allele or locus of interest can be directly sequenced using nucleic acid sequencing technologies.
  • Methods for nucleic acid sequencing are known in the art and include technologies provided by 454 Life Sciences (Branford, Conn.), Agencourt Bioscience (Beverly, Mass.), Applied Biosystems (Foster City, Calif.), LI-COR Biosciences (Lincoln, Nebr.), NimbleGen Systems (Madison, Wis.), Illumina (San Diego, Calif.), and VisiGen Biotechnologies (Houston, Tex.).
  • nucleic acid sequencing technologies comprise formats such as parallel bead arrays, sequencing by ligation, capillary electrophoresis, electronic microchips, “biochips,” microarrays, parallel microchips, and single-molecule arrays, as reviewed by R.F. Service Science 311:1544-1546, 2006.
  • Markers used in accordance with the present invention should preferably be diagnostic of origin in order for inferences to be made about subsequent populations.
  • SNP markers may be ideal for mapping because the likelihood that a particular SNP allele is derived from independent origins in the extant populations of a particular species is very low. As such, SNP markers appear to be useful for tracking and assisting introgression of alleles or loci.
  • plant includes plant cells, plant protoplasts, plant cells of tissue culture from which spinach plants can be regenerated, plant calli, plant clumps and plant cells that are intact in plants or parts of plants such as pollen, flowers, seeds, leaves, stems, and the like.
  • DM Downy mildew
  • DM or “downy mildew” refers to a disease of plants, such as spinach, caused by a pathogen from the genus Peronospora , in particular Peronospora farinosa f . sp. Spinaciae (Pfs).
  • race refers to an officially designated strain of Peronospora farinosa f . sp. spinaciae (Pfs) that can cause DM.
  • isolated refers to a newly occurring strain of Peronospora farinosa f . sp. spinaciae (Pfs) that can cause DM, and has not yet been officially named.
  • a spinach plant with resistance to DM according to the present invention carries a combination of alleles selected from A, C, and Vt.
  • the DM resistance may be to one or more known races of Peronospora farinosa f . sp.
  • spinaciae or may be to one or more isolates of Peronospora farinosa f . sp. spinaciae .
  • a plant of the invention may be defined as resistant to at least Peronospora farinosa f . sp. spinaciae Pfs 7, 8, 10, 11, 12, 13, and/or 14.
  • the terms “pedigree,” “population,” and “progeny” mean a collection of plants that share a common parental derivation.
  • variable means a group of similar plants that by their genetic pedigrees and performance can be identified from other varieties within the same species.
  • an “allele” refers to one of two or more alternative forms of a genomic sequence at a given locus on a chromosome.
  • a “Quantitative Trait Locus (QTL)” is a chromosomal location that encodes for at least a first allele that affects the expressivity of a phenotype.
  • a “marker” means a detectable characteristic that can be used to discriminate between organisms. Examples of such characteristics include, but are not limited to, genetic markers, biochemical markers, metabolites, morphological characteristics, and agronomic characteristics.
  • phenotype means the detectable characteristics of a cell or organism that can be influenced by gene expression.
  • the term “resistance” means evasion and/or reduction of pathogen infection by plant innate immunity, which can be shown by the absence and/or reduction of disease symptoms when compared to a susceptible plant.
  • the term “susceptible” means the infection of a plant by a pathogen, resulting in disease symptoms.
  • compatible interaction means the infection of a susceptible plant by a pathogen, resulting in disease symptoms.
  • the term “incompatible interaction” means the evasion and/or reduction of infection of a resistant plant by a pathogen, which can be shown by the absence and/or a reduction of disease symptoms.
  • the term “genotype” means the specific allelic makeup of a plant.
  • heterozygous phase means a diploid plant, such as spinach, that carries two distinct copies of an allele.
  • homozygous phase means a diploid plant, such as spinach, that carries two identical copies of an allele.
  • Introgressed when used in reference to a genetic locus, refers to a genetic locus that has been introduced into a new genetic background, such as through backcrossing. Introgression of a genetic locus can therefore be achieved through plant breeding methods and/or by molecular genetic methods.
  • molecular genetic methods include, but are not limited to, various plant transformation techniques and/or methods that provide for homologous recombination, non-homologous recombination, site-specific recombination, and/or genomic modifications that provide for locus substitution or locus conversion.
  • the term “linked,” when used in the context of nucleic acid markers and/or genomic regions, means that the markers and/or genomic regions are located on the same linkage group or chromosome such that they tend to segregate together at meiosis.
  • the term “denoting” when used in reference to a plant genotype refers to any method whereby a plant is indicated to have a certain genotype. This includes any means of identification of a plant having a certain genotype. Indication of a certain genotype may include, but is not limited to, any entry into any type of written or electronic medium or database whereby the plant's genotype is provided. Indications of a certain genotype may also include, but are not limited to, any method where a plant is physically marked or tagged. Illustrative examples of physical marking or tags useful in the invention include, but are not limited to, a barcode, a radio-frequency identification (RFID), a label, or the like.
  • RFID radio-frequency identification
  • a deposit was made of at least 2500 seeds of Spinacia oleracea accessions designated SMBS011-1162M, SMB-66-1143M, and SSB-66-1131M.
  • the deposits were made with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 USA.
  • ATCC American Type Culture Collection
  • the deposits were assigned ATCC Accession Nos. PTA-120472, PTA-12486, and PTA-12041, respectively.
  • the dates of deposit of these accessions were Jul. 17, 2013, Feb. 2, 2012, and Aug. 19, 2011, respectively. Access to the deposits will be available during the pendency of the application to persons entitled thereto upon request.
  • the deposits will be maintained in the ATCC Depository, which is a public depository, for a period of 30 years, or 5 years after the most recent request, or for the enforceable life of the patent, whichever is longer, and will be replaced if nonviable during that period. Applicant does not waive any infringement of their rights granted under this patent or any other form of variety protection, including the Plant Variety Protection Act (7 U.S.C. 2321 et seq.).
  • S. oleracea accessions in an internal genebank were screened.
  • publicly available spinach hybrids that were either fully susceptible, or carried a combination of resistance specificities were included in the trial as susceptible and resistance checks.
  • Infection was performed with Peronospora farinosa f . sp. spinaciae (Pfs) races 7, 8, and 10-14 to complement historic data on races 1-6. Race 9 is no longer present in the field.
  • Pfs Peronospora farinosa f . sp. spinaciae
  • a resistance-breaking isolate, collected in California (US) in the spring of 2013 was included. This isolate is currently referred to as UA4712 by the International Working Group on Peronospora and is a probable candidate for race Pfs 15.
  • Inbred line SMBS011-1162M carrying an allele identified as allele A
  • SMB-66-1143M included an allele designated Vt
  • SMB-66-1143M was shown to be resistant to new isolate UA4712, in addition to races 1-10.
  • Each of the identified alleles were found to confer DM resistance to different combinations of races.
  • the disease assay included 74 F3 families segregating for allele A, which were infected with Pfs race 8; 107 F3 families segregating for allele Vt challenged with races 7, 10, and 12; and 40 F3 families segregating for allele C, which were inoculated with race 10. Interestingly, when Vt-derived families demonstrated resistance to one race, immunity to the other two races was also observed.
  • sequence scaffolds Based on public information, the likely position of sequence scaffolds designated SF34732, SF59002, SF62749, SF63815, SF90906, SF95487, and SF178637 co-located with DM resistance.
  • Examples of nucleotide sequences corresponding to alleles C, A, and Vt conferring resistance to DM are provided as SEQ ID NOs:1-25.
  • polymorphisms between individual alleles of scaffolds are shown in FIG. 3 . Single nucleotide polymorphisms (SNPs) derived from these scaffolds were selected based on being polymorphic in one or more mapping populations.
  • the SNPs were converted to TaqMan (TM) assays and used for genotyping F2 individuals of the respective F3 families of each population. Linkage disequilibrium was tested, and the genetic distances among SNPs and phenotypes were estimated using Joinmap (Stam, Plant J 3:739-744, 1993). Association analysis confirmed linkage of sequence scaffolds and resistance by assembly of single groups. This result was found to be independent of the source or race used for mapping ( FIG. 1 ). Observed recombination frequencies and derived genetic distances varied due to the distinct sample size of each population. Scaffolds SF59002 and SF95487 appeared to co-segregate in every population.
  • Example 2 The genotype and phenotypes collected in Example 2 were used in a quantitative analysis with mapQTL, applying standard interval mapping settings (Van Ooijen, 1996). A major locus for resistance to Peronospora farinosa f . sp. spinaciae race 8 was detected in the mapping population segregating for allele A. Evidenced by a LOD peak of 57.51, the trait was highly associated with markers derived from scaffolds SF59002, SF95487, and SF63815 (Table 2). The locus appeared to have a major effect, explaining 97.2% of the observed variance.
  • DM resistance mapped to Chromosome 6 independent of the source or isolate used.
  • the resistance loci were delineated by common markers, on the distal position typically sequence scaffolds SF34732 and SF63815 and on the proximal position typically sequence scaffolds SF59002, SF95487 and SF90906.
  • the resistance alleles A, C and Vt were introduced into a susceptible hybrid.
  • the inbred SMBS011-1162M was used as a donors for allele A, the line SSB-66-1131M for Vt, and for allele C, SMB-66-1143M was used as a source.
  • Each of the alleles was introgressed separately into both inbred parents of the susceptible hybrid, following breeding methods known in the art.
  • a first spinach plant which is homozygous for allele A (A/A) was crossed to a second spinach plant (C/C) to generate a hybrid F1 which was heterozygous for alleles A and C ( FIG. 2A ).
  • This hybrid was referred to as Single Hybrid A, or as F1(A/C).
  • F1(A/C) was screened with known races and isolate UA4712 of Peronospora farinosa f . sp. spinaciae , as described in Example 5.
  • the hybrid was found to be resistant to all Pfs races, with the exception of race 13 (Table 7).
  • Hybrid A is also resistant to the newly emerging isolate UA4712.
  • Hybrid B carrying alleles C and Vt ( FIG. 2B ) was screened as described and found to be resistant to all Pfs races except Pfs 14 (Table 7). This is important, as Pfs race 14 does not occur in Europe.
  • a combination of alleles C and Vt in a spinach plant provides a fully resistant variety for the European market.
  • Hybrid C with alleles A and Vt was resistant to all Pfs races except isolate UA4712 (Table 7). This is also significant, since the distribution of a new isolate is initially limited to few locations. F1(A/Vt) is resistant to all currently named Pfs races.
  • Three-way hybrids were generated. Three-way hybrids are produced by crossing an F1 seed parent to an inbred parent P2. The F1 seed parent results from a cross between two near-isogenic lines of P1, each carrying a distinct resistance allele. The inbred parent P2 carries a third, complementary allele.
  • a three-way hybrid allows the deployment of all three identified alleles in a mixed population of diploid hybrid plants. Three versions of the 3-way hybrid are possible ( FIG. 2B ). Each cross results in a population of hybrid plants with resistance to all known Pfs races and isolate UA4712. However, the frequency of each allele will depend on how the three-way cross is structured.
  • Novel resistance originating from the genetic variety contained within cultivated spinach, Spinacia oleracea was identified. This resistance is surprising because genetic diversity in cultivated crops is typically narrow (Fernie et al., Curr. Opinion P 1. Biol. 9:196-202, 2006).
  • the identification of the three unique resistance alleles, A, Vt, and/or C, in the three spinach lines provides for race-specific DM resistance breeding, with only intra-specific S. oleracea crosses. Additionally, these alleles allow stacking of resistance in single hybrid combinations that are unsurpassed in combining novel attributes, including resistance to all known Pfs races, to the new isolate UA4712, or resistance to all described European DM populations. Markers associated with the three resistance alleles allow introduction of the described and other DM-resistance alleles in any cultivated spinach hybrid. Finally, a three-way hybrid method is disclosed to allow for the development of additional DM resistant varieties.
  • Races of Peronospora farinosa f . sp. spinaciae are maintained on living host plants, obtainable from Naktuinbouw (P.O. Box 40, NL-2370 AA, Roelofarendsveen, Netherlands, naktuinbouw.com), or plant material with spores stored at ⁇ 20° C. for a maximum of one year.
  • Method of inoculation Sporulating leaves, taken from host plants that were infected seven days before, are thoroughly rinsed with sterile tap water (maximum 150 ml water per 224 plants). The spore suspension is filtered through cheesecloth and sprayed on test plants until the inoculum covers the leaves but does not run off. 150 ml of suspension is enough for up to 3 ⁇ 224 plants. Spore density should be 20,000 to 100,000 conidia/ml water. The spore suspension should be used fresh. As spinach downy mildew is wind-borne, sporulating plants should be kept in closed containers or isolated chambers to prevent any cross-contamination.
  • Resistant controls are needed in each multiplication and in each test to ensure the race identity. Light and humidity conditions during seedling development and incubation are critical. Optimal humidity of approximately 80-90% RH allows plant growth and fungal growth; strong light inhibits spore germination and infection.
  • the test should be carried out in wintertime with protection against direct sunshine. After inoculation, the plants should remain under plastic for three days. After this time, the plastic should be slightly raised during the daytime.
  • Races Pfs: 1-8 and 10-13 of Peronospora farinosa f . sp. spinaciae are defined with a standard set of “differential varieties” according to Table 8.

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